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chicane  

Capture Hi-C Analysis Engine
View on CRAN: Click here


Download and install chicane package within the R console
Install from CRAN:
install.packages("chicane")

Install from Github:
library("remotes")
install_github("cran/chicane")

Install by package version:
library("remotes")
install_version("chicane", "0.1.8")



Attach the package and use:
library("chicane")
Maintained by
Syed Haider
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-08-30
Latest Update: 2021-11-06
Description:
Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
How to cite:
Syed Haider (2018). chicane: Capture Hi-C Analysis Engine. R package version 0.1.8, https://cran.r-project.org/web/packages/chicane
Previous versions and publish date:
0.1.0 (2018-08-30 15:20), 0.1.1 (2019-10-01 21:20), 0.1.2 (2020-07-28 01:00), 0.1.3 (2021-01-13 19:20), 0.1.4 (2021-03-24 14:30), 0.1.5 (2021-06-10 09:00), 0.1.6 (2021-07-25 16:50), 0.1.7 (2021-09-21 15:10)
Other packages that cited chicane R package
View chicane citation profile
Other R packages that chicane depends, imports, suggests or enhances
Functions, R codes and Examples using the chicane R package
Some associated functions: add.covariates . add.fragment.coordinates . bedtools.installed . bre80 . check.model.numerical.fit . check.split.data.numerical.fit . chicane . combine.replicates . compare.replicates . convert.bam . convert.hicup.digest.bed . convert.standard.format . convert.to.one.based . create.locus.plot . create.modelfit.plot . distance.bin . distance.split . fill.in.zeros . filter.fragments . fit.glm . fit.model . get.combination.count . get.components . get.distance . get.id.components . get.interaction.id . get.trans.counts . is.glm.nb.maxiter.warning . is.glm.nb.theta.error . is.glm.nb.theta.warning . model.rows.sanity.check . model.try.catch . multiple.testing.correct . prepare.data . read.bed . run.model.fitting . smart.split . stratified.enrichment.sample . test.enrichment . verify.interaction.data . 
Some associated R codes: add.covariates.R . add.fragment.coordinates.R . bedtools.installed.R . bre80.R . check.model.numerical.fit.R . check.split.data.numerical.fit.R . chicane-pkg.R . chicane.R . combine.replicates.R . compare.replicates.R . convert.bam.R . convert.hicup.digest.bed.R . convert.standard.format.R . convert.to.one.based.R . create.locus.plot.R . create.modelfit.plot.R . distance.bin.R . distance.split.R . fill.in.zeros.R . filter.fragments.R . fit.glm.R . fit.model.R . get.combination.count.R . get.components.R . get.distance.R . get.id.components.R . get.interaction.id.R . get.trans.counts.R . is.glm.nb.maxiter.warning.R . is.glm.nb.theta.error.R . is.glm.nb.theta.warning.R . model.rows.sanity.check.R . model.try.catch.R . multiple.testing.correct.R . prepare.data.R . read.bed.R . run.model.fitting.R . smart.split.R . stratified.enrichment.sample.R . test.enrichment.R . verify.interaction.data.R .  Full chicane package functions and examples
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